PNMA6F

Summary

PNMA6F (PNMA family member 6F, HGNC:53119) is a protein-coding gene on chromosome Xq28, encoding Paraneoplastic antigen Ma6F (A0A0J9YX94).

At a glance

• Clinical variants (ClinVar): 3 total
• MANE Select transcript: NM_001354980

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53119
Approved symbol	PNMA6F
Name	PNMA family member 6F
Location	Xq28
Locus type	gene with protein product
Status	Approved
Aliases	PNMA6BL
Ensembl gene	ENSG00000225110
Ensembl biotype	protein_coding
Entrez	105373377

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000436629

RefSeq mRNA: 1 — MANE Select: NM_001354980 NM_001354980

CCDS: CCDS87792

Canonical transcript exons

ENST00000436629 — 2 exons

Exon	Start	End
ENSE00001716565	153317680	153320757
ENSE00003777813	153321552	153321767

Expression profiles

Bgee: expression breadth broad, 37 present calls, max score 83.78.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0377 / max 14.3536, expressed in 24 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
200862	0.0377	24

Top tissues by expression

124 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
hypothalamus	UBERON:0001898	83.78	gold quality
prefrontal cortex	UBERON:0000451	74.60	gold quality
anterior cingulate cortex	UBERON:0009835	74.25	gold quality
frontal cortex	UBERON:0001870	72.22	gold quality
nucleus accumbens	UBERON:0001882	72.14	gold quality
superior frontal gyrus	UBERON:0002661	72.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	71.34	gold quality
Brodmann (1909) area 9	UBERON:0013540	71.21	gold quality
cerebral cortex	UBERON:0000956	70.03	gold quality
right frontal lobe	UBERON:0002810	68.53	gold quality
temporal lobe	UBERON:0001871	66.85	gold quality
amygdala	UBERON:0001876	66.52	gold quality
substantia nigra	UBERON:0002038	63.91	gold quality
Ammon’s horn	UBERON:0001954	62.39	gold quality
brain	UBERON:0000955	60.94	gold quality
caudate nucleus	UBERON:0001873	58.25	gold quality
primary visual cortex	UBERON:0002436	57.74	gold quality
putamen	UBERON:0001874	54.02	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	49.97	gold quality
cortical plate	UBERON:0005343	43.29	gold quality
pituitary gland	UBERON:0000007	41.54	gold quality
adenohypophysis	UBERON:0002196	40.29	gold quality
ventricular zone	UBERON:0003053	39.86	gold quality
left adrenal gland cortex	UBERON:0035825	39.56	gold quality
left adrenal gland	UBERON:0001234	38.53	gold quality
adrenal gland	UBERON:0002369	38.40	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ganglionic eminence	UBERON:0004023	37.14	gold quality
right adrenal gland	UBERON:0001233	36.24	gold quality
bone marrow cell	CL:0002092	36.16	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.30

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pnma6e	ENSMUSG00000096966
mus_musculus	Gm45015	ENSMUSG00000109368
rattus_norvegicus	Pnma6e	ENSRNOG00000070467

Paralogs (13): MOAP1 (ENSG00000165943), ZCCHC18 (ENSG00000166707), CCDC8 (ENSG00000169515), ZCCHC12 (ENSG00000174460), PNMA1 (ENSG00000176903), PNMA8A (ENSG00000182013), PNMA3 (ENSG00000183837), PNMA5 (ENSG00000198883), PNMA8B (ENSG00000204851), PNMA6E (ENSG00000214897), PNMA6A (ENSG00000235961), PNMA2 (ENSG00000240694), PNMA8C (ENSG00000277531)

Protein

Protein identifiers

Paraneoplastic antigen Ma6F — A0A0J9YX94 (reviewed: A0A0J9YX94)

All UniProt accessions (1): A0A0J9YX94

RefSeq proteins (1): NP_001341909* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026523	PNMA	Family
IPR048270	PNMA_C	Domain
IPR048271	PNMA_N	Domain

Pfam: PF14893, PF20846

UniProt features (10 total): compositionally biased region 7, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A0J9YX94-F1	61.09	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 4 (showing top): chrXq28, DESCARTES_MAIN_FETAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_ADRENAL_SLC26A4_PAEP_POSITIVE_CELLS, DESCARTES_FETAL_CEREBELLUM_SLC24A4_PEX5L_POSITIVE_CELLS

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

562 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PNMA6F	CDR2L	Q86X02	507
PNMA6F	CCDC8	Q9H0W5	418
PNMA6F	PNMA8B	Q9ULN7	283
PNMA6F	PNMA8A	Q86V59	272
PNMA6F	ZCCHC18	P0CG32	242
PNMA6F	CASKIN1	Q8WXD9	241
PNMA6F	PNMA8C	A0A1B0GUJ8	206
PNMA6F	TRIM39	Q9HCM9	192
PNMA6F	ZCCHC12	Q6PEW1	185
PNMA6F	RASSF6	Q6ZTQ3	184
PNMA6F	PNMA5	Q96PV4	174
PNMA6F	PRUNE2	Q8WUY3	167
PNMA6F	EXOSC9	Q06265	166
PNMA6F	DENR	O43583	164
PNMA6F	PNMA1	Q8ND90	160

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A5D7L8, A6NDY0, A6NKD2, A7E321, E9PGG2, F6SZT2, O14771, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P17564, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q2M329, Q587J8, Q5DTT8, Q5R5G8, Q5R6R8, Q5SV97, Q60465, Q62881, Q69ZB3, Q6P752, Q86V59, Q8BSI6, Q8IWY8, Q8N3D4, Q8VD63

Diamond homologs: A0A0J9YX94, A0A0J9YXQ4, A0A1B0GUJ8, A6QLK5, A7E321, P0CG32, P0CW24, Q08DL1, Q2KIT6, Q5HZA3, Q5R6R8, Q6PEW1, Q80VM8, Q86V59, Q8JZW8, Q8ND90, Q8VD24, Q8VHZ4, Q9CZA5, Q9UL41, Q9ULN7, D3YZV8, P62521, Q5DTT8, Q5R486, Q8BHK0, Q8C1C8, Q95KI4, Q96BY2, Q96PV4, Q9ERH6, Q9GMU3, Q9H0W5, Q9UL42

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

3 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

451 predictions. Top by Δscore:

Variant	Effect	Δscore
X:153320577:T:TA	donor_gain	1.0000
X:153320588:ATGTT:A	donor_gain	1.0000
X:153320758:C:CC	acceptor_gain	1.0000
X:153321430:T:TA	donor_gain	1.0000
X:153321550:A:AC	donor_gain	1.0000
X:153321551:C:CC	donor_gain	1.0000
X:153320754:CAGC:C	acceptor_gain	0.9900
X:153320757:CCTG:C	acceptor_loss	0.9900
X:153320758:CT:C	acceptor_loss	0.9900
X:153320764:G:GC	acceptor_gain	0.9900
X:153320767:C:CT	acceptor_gain	0.9900
X:153321427:T:TA	donor_gain	0.9900
X:153321465:C:CA	donor_gain	0.9900
X:153321478:A:AC	donor_gain	0.9900
X:153321479:C:CC	donor_gain	0.9900
X:153321551:CTTT:C	donor_gain	0.9900
X:153320546:G:A	donor_gain	0.9800
X:153320755:AGC:A	acceptor_gain	0.9800
X:153320764:G:C	acceptor_gain	0.9800
X:153320768:A:T	acceptor_gain	0.9800
X:153321554:T:A	donor_gain	0.9800
X:153321578:C:CT	donor_gain	0.9800
X:153321633:AGAGG:A	donor_gain	0.9800
X:153321665:G:A	donor_gain	0.9800
X:153320592:T:TA	donor_gain	0.9700
X:153320756:GC:G	acceptor_gain	0.9700
X:153320757:CC:C	acceptor_gain	0.9700
X:153321407:T:TA	donor_gain	0.9700
X:153321524:CT:C	donor_gain	0.9700
X:153321579:C:CT	donor_gain	0.9700

AlphaMissense

3705 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:153319604:G:C	F357L	0.982
X:153319604:G:T	F357L	0.982
X:153319606:A:G	F357L	0.982
X:153319907:A:C	F256L	0.975
X:153319907:A:T	F256L	0.975
X:153319909:A:G	F256L	0.975
X:153319685:A:C	F330L	0.969
X:153319685:A:T	F330L	0.969
X:153319687:A:G	F330L	0.969
X:153320582:G:C	F31L	0.961
X:153320582:G:T	F31L	0.961
X:153320584:A:G	F31L	0.961
X:153319590:T:A	E362V	0.954
X:153319436:G:C	F413L	0.946
X:153319436:G:T	F413L	0.946
X:153319438:A:G	F413L	0.946
X:153320583:A:G	F31S	0.945
X:153320480:G:C	F65L	0.944
X:153320480:G:T	F65L	0.944
X:153320482:A:G	F65L	0.944
X:153320493:G:T	A61D	0.934
X:153320519:G:C	F52L	0.933
X:153320519:G:T	F52L	0.933
X:153320521:A:G	F52L	0.933
X:153319859:C:A	W272C	0.929
X:153319859:C:G	W272C	0.929
X:153320422:A:G	W85R	0.924
X:153320422:A:T	W85R	0.924
X:153320619:A:G	I19T	0.923
X:153319631:C:A	Q348H	0.918

dbSNP variants (sampled 300 via entrez): RS1000351416 (X:153319151 G>A,T), RS1002123304 (X:153318230 A>G), RS1002537967 (X:153318411 G>T), RS1002754672 (X:153320689 C>A), RS1003218606 (X:153321090 C>G,T), RS1003805708 (X:153319665 A>C,T), RS1004070537 (X:153318462 G>A,C), RS1004122897 (X:153318712 T>A), RS1006164547 (X:153319677 C>T), RS1006970056 (X:153320239 C>T), RS1007330094 (X:153320019 C>T), RS1008591890 (X:153321584 G>A,T), RS1009787377 (X:153319160 C>A), RS1009880884 (X:153319390 A>T), RS1010559650 (X:153322861 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
benzo(e)pyrene	increases methylation	1
Methapyrilene	increases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.